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Initialize demo with Isilon storage solution (#1)
* initialize files for work * linting * observe performance * linting and docs * changes based on feedback Co-Authored-By: Cameron Mattson <[email protected]> --------- Co-authored-by: Cameron Mattson <[email protected]>
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‎.gitignore

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# PyPI configuration file
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.pypirc
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# data ignores
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src/demo/data/

‎.pre-commit-config.yaml

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# See https://pre-commit.com for more information
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# See https://pre-commit.com/hooks.html for more hooks
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default_language_version:
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python: python3.11
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repos:
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v5.0.0
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hooks:
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- id: trailing-whitespace
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- id: end-of-file-fixer
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- id: check-yaml
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- id: check-added-large-files
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- id: detect-private-key
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- repo: https://github.com/tox-dev/pyproject-fmt
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rev: "v2.5.0"
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hooks:
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- id: pyproject-fmt
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- repo: https://github.com/citation-file-format/cffconvert
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rev: 5295f87c0e261da61a7b919fc754e3a77edd98a7
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hooks:
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- id: validate-cff
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- repo: https://github.com/codespell-project/codespell
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rev: v2.3.0
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hooks:
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- id: codespell
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exclude: |
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(?x)^(
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.*\.ipynb |
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justfile |
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.*\.cff
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)$
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- repo: https://github.com/executablebooks/mdformat
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rev: 0.7.21
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hooks:
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- id: mdformat
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additional_dependencies:
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- mdformat-gfm
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- repo: https://github.com/adrienverge/yamllint
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rev: v1.35.1
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hooks:
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- id: yamllint
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exclude: pre-commit-config.yaml
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- repo: https://github.com/astral-sh/ruff-pre-commit
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rev: "v0.9.2"
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hooks:
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- id: ruff-format
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- id: ruff
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- repo: https://github.com/rhysd/actionlint
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rev: v1.7.6
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hooks:
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- id: actionlint
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- repo: https://gitlab.com/vojko.pribudic.foss/pre-commit-update
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rev: v0.6.0
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hooks:
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- id: pre-commit-update
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args: ["--keep", "mdformat", "--keep", "pre-commit-update", "--keep", "cffconvert"]

‎CITATION.cff

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# This CITATION.cff file was generated with cffinit.
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# Visit https://bit.ly/cffinit to generate yours today!
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---
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cff-version: 1.2.0
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title: demo-uca-isilon-python
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message: >-
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If you use this software, please cite it using the
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metadata from this file.s
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type: software
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authors:
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- given-names: Dave
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family-names: Bunten
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orcid: 'https://orcid.org/0000-0001-6041-3665'
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repository-code: 'https://github.com/WayScience/demo-uca-isilon-python'
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abstract: >-
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Demonstrating capabilities with the University of Colorado Anschutz
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(UCA) Isilon storage solution using Python.
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keywords:
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- python
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- storage
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- isilon
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- demonstration
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license: BSD-3-Clause
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references:
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- title: >-
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Plate 2 (Cell Painting images from Plate 2 for NF1_cellpainting_data project)
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type: data
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url: https://figshare.com/articles/dataset/Plate_2/22233700
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notes: >-
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Image data for related NF1_cellpainting_data parquet sqlite.
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authors:
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- family-names: Tomkinson
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given-names: Jenna
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- family-names: Mattson-Hoss
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given-names: Michelle
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- family-names: Sarnoff
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given-names: Herb
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- family-names: Way
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given-names: Gregory
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date-published: "2023-04-12"
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identifiers:
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- type: doi
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value: 10.6084/m9.figshare.22233700.v4

‎CODE_OF_CONDUCT.md

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# Contributor Covenant Code of Conduct
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## Our Pledge
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We as members, contributors, and leaders pledge to make participation in our
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community a harassment-free experience for everyone, regardless of age, body
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nationality, personal appearance, race, caste, color, religion, or sexual
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identity and orientation.
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We pledge to act and interact in ways that contribute to an open, welcoming,
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diverse, inclusive, and healthy community.
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Examples of behavior that contributes to a positive environment for our
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Community leaders are responsible for clarifying and enforcing our standards of
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Community leaders will follow these Community Impact Guidelines in determining
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Violating these terms may lead to a permanent ban.
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## Attribution
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This Code of Conduct is adapted from the [Contributor Covenant][homepage],
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version 2.1, available at
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[https://www.contributor-covenant.org/version/2/1/code_of_conduct.html][v2.1].
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Community Impact Guidelines were inspired by
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[Mozilla's code of conduct enforcement ladder][mozilla coc].
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For answers to common questions about this code of conduct, see the FAQ at
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[https://www.contributor-covenant.org/faq][faq]. Translations are available at
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[https://www.contributor-covenant.org/translations][translations].
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[faq]: https://www.contributor-covenant.org/faq
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[homepage]: https://www.contributor-covenant.org
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[mozilla coc]: https://github.com/mozilla/diversity
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[translations]: https://www.contributor-covenant.org/translations
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[v2.1]: https://www.contributor-covenant.org/version/2/1/code_of_conduct.html

‎LICENSE

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BSD 3-Clause License
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Copyright (c) 2025, The Way Lab
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Copyright (c) 2024, The Way Lab
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Redistribution and use in source and binary forms, with or without
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modification, are permitted provided that the following conditions are met:

‎README.md

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# demo-uca-isilon-python
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Demonstrating capabilities with the University of Colorado Anschutz (UCA) Isilon storage solution using Python.
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# University of Colorado Anschutz Isilon with Python Demonstration
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This repository demonstrates using the [University of Colorado Anschutz Isilon](https://www.cuanschutz.edu/offices/office-of-information-technology/tools-services/storage-servers-and-backups) storage solution with Python.
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We seek to understand how this works and how it performs more generally.
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Our approach here focuses on mounting the Isilon path to a local directory on a machine, then performing work using that mounted directory.
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## Development
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1. [Install `uv`](https://docs.astral.sh/uv/getting-started/installation/).
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1. [Install `just`](https://github.com/casey/just?tab=readme-ov-file#installation).
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1. Install package locally (e.g. `uv pip install -e "."`).
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1. Run various other tasks using [just](https://github.com/casey/just) (e.g. `just tiff_to_omezarr`)
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## Tasks
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[Just](https://github.com/casey/just) tasks may be run to help generate results without needing to run individual files or perform additional discovery within this project.
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You can show all available tasks with `just` (which lists all tasks).
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Examples:
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```bash
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just run-isilon-demo
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```
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## Isilon notes
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- Isilon requires you to have access through the UCA VPN or local campus network.
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- Isilon may be mounted on MacOS using `mount_smbfs`.
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- Using a mount path without a username or password specified will attempt to mount the directory using your MacOS user which is currently logged in (which may differ from your UCA account credentials).
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- Isilon may be mounted on Linux using `mount -t cifs`.

‎justfile

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# justfile for common project commands
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# see here for more information: https://github.com/casey/just
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# find system default shell
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hashbang := if os() == 'macos' {
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'/usr/bin/env zsh'
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} else {
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'/usr/bin/env bash'
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}
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# cifs / samba command based on operating system
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cifs_or_samba_mount_command := if os() == 'macos' {
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'mount_smbfs //data.ucdenver.pvt/dept/SOM/SOMDean/Testing/DBMITest ~/mnt/isilon'
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} else {
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'sudo mount -t cifs //data.ucdenver.pvt/dept/SOM/SOMDean/Testing/DBMITest -o username='
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}
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# show a list of just commands for this project
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default:
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@just --list
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# install the project for development purposes
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@setup:
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#!{{hashbang}}
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uv pip install '.'
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# mount a uca cifs / samba
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@mount-isilon:
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#!{{hashbang}}
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if mount | grep "/mnt/isilon"; then
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echo "The isilon fileshare is already mounted."
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else
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# create a mount destination
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mkdir -p ~/mnt/isilon
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# run the mount command
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{{cifs_or_samba_mount_command}}
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fi
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# run isilon demo
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@run-isilon-demo:
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#!{{hashbang}}
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# mount isilon
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just mount-isilon
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# prepare the data
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uv run python src/demo/prepare_files.py
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# run the test, storing the results in a notebook
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uv run papermill src/demo/demo.ipynb src/demo/demo.ipynb
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# share a friendly message
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echo "Demo completed. The results are stored in src/demo/demo.ipynb."

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